Janet Young
A repository to share bioinformatics teaching materials with the Malik lab.
Available via github, here.
My own local copy is in /fh/fast/malik_h/user/jayoung/git_more_repos/MalikLab_bioinformaticsResources
WARNING - some of these files contain notes I put together for an individual project, some a long time ago. In many cases they're probably out-of-date: there might be better ways to do things now.
Just let me know! You can talk to me, email me, or submit a github issue if that's your thing.
I usually have in-person chats to help you learn these things, and we use these notes for reference. They might not make sense on their own.
- To learn how to use the Hutch compute cluster
- To learn some basic unix commands
- Some general advice on bioinformatics, and suggestions for where you might learn more
- Some more advanced tricks for the Hutch compute cluster
- Notes on transferring/copying large files from one computer to another
- Some bioinformatics tools you can use via the command-line, especially blast and phyml.
- Some old notes on tools to analyze deep sequencing data. I think you'll get better information elsewhere.
There's a lot of material out there to help you learn bioinformatics, a lot of it better than anything I could put together.
Some suggestions for tutorials, etc are here - let me know if you have any you'd like to add.
Join the Hutch FH-Data/FH-BCR Slack workspace (old/new names for the same thing) - see instructions on joining here. Once you're in, browse the channels for groups that interest you. It's a great place to ask for help on anything from R coding to analysis strategies - very supportive community.
We have a Dropbox folder called PAML_class with documents to help teach/learn PAML. If you don't already have access, let me know. I might transfer those materials here at some point - will see how it goes sharing the other notes first.
These are notes for myself - I haven't written these in a way that will be clear to others, but you're welcome to look through them if you like.